X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=f5ea12efe645811fb1777731088d4e251c205a2f;hb=8ec36c3e36ff5beb0db07345babe8c8426d0426b;hp=d530fd8f8c0b4559dbeee66172cc078bc289e230;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index d530fd8..f5ea12e 100755 --- a/src/jalview/appletgui/IdCanvas.java +++ b/src/jalview/appletgui/IdCanvas.java @@ -1,28 +1,38 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.awt.*; +import jalview.datamodel.SequenceI; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; -import jalview.datamodel.*; +import java.awt.Color; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.Panel; +import java.beans.PropertyChangeEvent; +import java.util.List; -public class IdCanvas extends Panel +public class IdCanvas extends Panel implements ViewportListenerI { protected AlignViewport av; @@ -40,17 +50,18 @@ public class IdCanvas extends Panel boolean fastPaint = false; - java.util.Vector searchResults; + List searchResults; public IdCanvas(AlignViewport av) { setLayout(null); this.av = av; PaintRefresher.Register(this, av.getSequenceSetId()); + av.getRanges().addPropertyChangeListener(this); } - public void drawIdString(Graphics gg, SequenceI s, int i, int starty, - int ypos) + public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s, + int i, int starty, int ypos) { int charHeight = av.getCharHeight(); @@ -81,7 +92,7 @@ public class IdCanvas extends Panel ((i - starty) * charHeight) + ypos + charHeight - (charHeight / 5)); - if (av.hasHiddenRows && av.showHiddenMarkers) + if (hiddenRows) { drawMarker(i, starty, ypos); } @@ -90,34 +101,38 @@ public class IdCanvas extends Panel public void fastPaint(int vertical) { - if (gg == null) + if (gg == null || av.getWrapAlignment()) { repaint(); return; } - gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical - * av.charHeight); + ViewportRanges ranges = av.getRanges(); - int ss = av.startSeq, es = av.endSeq, transY = 0; + gg.copyArea(0, 0, getSize().width, imgHeight, 0, + -vertical * av.getCharHeight()); + + int ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transY = 0; if (vertical > 0) // scroll down { ss = es - vertical; - if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time + if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page + // at a + // time { - ss = av.startSeq; + ss = ranges.getStartSeq(); } else { - transY = imgHeight - vertical * av.charHeight; + transY = imgHeight - ((vertical + 1) * av.getCharHeight()); } } else if (vertical < 0) { es = ss - vertical; - if (es > av.endSeq) + if (es > ranges.getEndSeq()) { - es = av.endSeq; + es = ranges.getEndSeq(); } } @@ -131,11 +146,13 @@ public class IdCanvas extends Panel repaint(); } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { if (getSize().height < 0 || getSize().width < 0) @@ -150,7 +167,7 @@ public class IdCanvas extends Panel } imgHeight = getSize().height; - imgHeight -= imgHeight % av.charHeight; + imgHeight -= imgHeight % av.getCharHeight(); if (imgHeight < 1) { @@ -166,146 +183,177 @@ public class IdCanvas extends Panel // Fill in the background gg.setColor(Color.white); - Font italic = new Font(av.getFont().getName(), Font.ITALIC, av - .getFont().getSize()); + Font italic = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); gg.setFont(italic); gg.fillRect(0, 0, getSize().width, getSize().height); - drawIds(av.startSeq, av.endSeq); + drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq()); g.drawImage(image, 0, 0, this); } + /** + * local copy of av.getCharHeight set at top of drawIds + */ + private int avcharHeight; + void drawIds(int starty, int endy) { - Font italic = new Font(av.getFont().getName(), Font.ITALIC, av - .getFont().getSize()); - - gg.setFont(italic); + avcharHeight = av.getCharHeight(); Color currentColor = Color.white; Color currentTextColor = Color.black; + final boolean doHiddenCheck = av.isDisplayReferenceSeq() + || av.hasHiddenRows(); + boolean hiddenRows = av.hasHiddenRows() && av.getShowHiddenMarkers(); + if (av.getWrapAlignment()) { - int maxwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight(); + drawIdsWrapped(starty, doHiddenCheck, hiddenRows); + return; + } - if (av.hasHiddenColumns) + // Now draw the id strings + SequenceI seq; + for (int i = starty; i <= endy; i++) + { + seq = av.getAlignment().getSequenceAt(i); + if (seq == null) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + continue; } - - int annotationHeight = 0; - AnnotationLabels labels = null; - - if (av.showAnnotation) + // hardwired italic IDs in applet currently + Font italic = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + gg.setFont(italic); + // boolean isrep=false; + if (doHiddenCheck) { - AnnotationPanel ap = new AnnotationPanel(av); - annotationHeight = ap.adjustPanelHeight(); - labels = new AnnotationLabels(av); + // isrep = + setHiddenFont(seq); } - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + // Selected sequence colours + if ((searchResults != null) && searchResults.contains(seq)) + { + currentColor = Color.black; + currentTextColor = Color.white; + } + else if ((av.getSelectionGroup() != null) + && av.getSelectionGroup().getSequences(null).contains(seq)) + { + currentColor = Color.lightGray; + currentTextColor = Color.black; + } + else { - hgap += av.charHeight; + currentColor = av.getSequenceColour(seq); + currentTextColor = Color.black; } - int cHeight = alheight * av.charHeight + hgap + annotationHeight; + gg.setColor(currentColor); + // TODO: isrep could be used to highlight the representative in a + // different way + gg.fillRect(0, (i - starty) * avcharHeight, getSize().width, + avcharHeight); + gg.setColor(currentTextColor); - int rowSize = av.getEndRes() - av.getStartRes(); + gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0, + (((i - starty) * avcharHeight) + avcharHeight) + - (avcharHeight / 5)); - // Draw the rest of the panels - for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height) - && (row < maxwidth); ypos += cHeight, row += rowSize) + if (hiddenRows) { - for (int i = starty; i < alheight; i++) - { + drawMarker(i, starty, 0); + } + } + } - SequenceI s = av.alignment.getSequenceAt(i); - gg.setFont(italic); - if (av.hasHiddenRows) - { - setHiddenFont(s); - } - drawIdString(gg, s, i, 0, ypos); - } + /** + * Draws sequence ids in wrapped mode + * + * @param starty + * @param doHiddenCheck + * @param hiddenRows + */ + protected void drawIdsWrapped(int starty, final boolean doHiddenCheck, + boolean hiddenRows) + { + int maxwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight(); - if (labels != null) - { - gg.translate(0, ypos + (alheight * av.charHeight)); - labels.drawComponent(gg, getSize().width); - gg.translate(0, -ypos - (alheight * av.charHeight)); - } + if (av.hasHiddenColumns()) + { + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; + } - } + int annotationHeight = 0; + AnnotationLabels labels = null; + + if (av.isShowAnnotation()) + { + AnnotationPanel ap = new AnnotationPanel(av); + annotationHeight = ap.adjustPanelHeight(); + labels = new AnnotationLabels(av); } - else + int hgap = avcharHeight; + if (av.getScaleAboveWrapped()) { - // Now draw the id strings - SequenceI seq; - for (int i = starty; i < endy; i++) - { + hgap += avcharHeight; + } - seq = av.alignment.getSequenceAt(i); - if (seq == null) - { - continue; - } - gg.setFont(italic); - // boolean isrep=false; - if (av.hasHiddenRows) - { - // isrep = - setHiddenFont(seq); - } + int cHeight = alheight * avcharHeight + hgap + annotationHeight; - // Selected sequence colours - if ((searchResults != null) && searchResults.contains(seq)) - { - currentColor = Color.black; - currentTextColor = Color.white; - } - else if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null).contains(seq)) - { - currentColor = Color.lightGray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; - } + int rowSize = av.getRanges().getViewportWidth(); - gg.setColor(currentColor); - // TODO: isrep could be used to highlight the representative in a - // different way - gg.fillRect(0, (i - starty) * av.charHeight, getSize().width, - av.charHeight); - gg.setColor(currentTextColor); + // hardwired italic IDs in applet currently + Font italic = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + gg.setFont(italic); - gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0, - (((i - starty) * av.charHeight) + av.charHeight) - - (av.charHeight / 5)); + /* + * draw repeating sequence ids until out of sequence data or + * out of visible space, whichever comes first + */ + int ypos = hgap; + int row = av.getRanges().getStartRes(); + while ((ypos <= getHeight()) && (row < maxwidth)) + { + for (int i = starty; i < alheight; i++) + { - if (av.hasHiddenRows && av.showHiddenMarkers) + SequenceI s = av.getAlignment().getSequenceAt(i); + // gg.setFont(italic); + if (doHiddenCheck) { - drawMarker(i, starty, 0); + setHiddenFont(s); } + drawIdString(gg, hiddenRows, s, i, 0, ypos); + } + + if (labels != null) + { + gg.translate(0, ypos + (alheight * avcharHeight)); + labels.drawComponent(gg, getSize().width); + gg.translate(0, -ypos - (alheight * avcharHeight)); } + ypos += cHeight; + row += rowSize; } } - public void setHighlighted(java.util.Vector found) + public void setHighlighted(List list) { - searchResults = found; + searchResults = list; repaint(); } void drawMarker(int i, int starty, int yoffset) { - SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences; + SequenceI[] hseqs = av.getAlignment() + .getHiddenSequences().hiddenSequences; // Use this method here instead of calling hiddenSeq adjust // 3 times. int hSize = hseqs.length; @@ -339,36 +387,75 @@ public class IdCanvas extends Panel gg.setColor(Color.blue); if (below) { - gg.fillPolygon(new int[] - { getSize().width - av.charHeight, getSize().width - av.charHeight, - getSize().width }, new int[] - { (i - starty) * av.charHeight + yoffset, - (i - starty) * av.charHeight + yoffset + av.charHeight / 4, - (i - starty) * av.charHeight + yoffset }, 3); + gg.fillPolygon( + new int[] + { getSize().width - avcharHeight, + getSize().width - avcharHeight, getSize().width }, + new int[] + { (i - starty) * avcharHeight + yoffset, + (i - starty) * avcharHeight + yoffset + avcharHeight / 4, + (i - starty) * avcharHeight + yoffset }, + 3); } if (above) { - gg.fillPolygon(new int[] - { getSize().width - av.charHeight, getSize().width - av.charHeight, - getSize().width }, new int[] - { (i - starty + 1) * av.charHeight + yoffset, - (i - starty + 1) * av.charHeight + yoffset - av.charHeight / 4, - (i - starty + 1) * av.charHeight + yoffset }, 3); + gg.fillPolygon( + new int[] + { getSize().width - avcharHeight, + getSize().width - avcharHeight, getSize().width }, + new int[] + { (i - starty + 1) * avcharHeight + yoffset, + (i - starty + 1) * avcharHeight + yoffset + - avcharHeight / 4, + (i - starty + 1) * avcharHeight + yoffset }, + 3); } } boolean setHiddenFont(SequenceI seq) { - Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont() - .getSize()); + Font bold = new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); - if (av.hiddenRepSequences != null - && av.hiddenRepSequences.containsKey(seq)) + if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) { gg.setFont(bold); return true; } return false; } + + /** + * Respond to viewport range changes (e.g. alignment panel was scrolled). Both + * scrolling and resizing change viewport ranges. Scrolling changes both start + * and end points, but resize only changes end values. Here we only want to + * fastpaint on a scroll, with resize using a normal paint, so scroll events + * are identified as changes to the horizontal or vertical start value. + *

+ * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll + * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is + * provided, but it generates a change of "startres" which does require an + * update here. + */ + @Override + public void propertyChange(PropertyChangeEvent evt) + { + String propertyName = evt.getPropertyName(); + if (propertyName.equals(ViewportRanges.STARTSEQ) + || (av.getWrapAlignment() + && propertyName.equals(ViewportRanges.STARTRES))) + { + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ)) + { + fastPaint(((int[]) evt.getNewValue())[1] + - ((int[]) evt.getOldValue())[1]); + } + else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); + } + } }